#############################################################################################

#This script gets all scripts of diversity using 8 arthropods order at multi-hierarchical levels 
#We used 8 groups: Arachnda, Coleoptera, Collembola, Diptera, Hemiptera, Hymenoptera, Lepidoptera, and Myriapoda. 

library(stats)
library(base)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(dplyr)
library(tidyr)
library (knitr)
library(PMCMR)
## PMCMR is superseded by PMCMRplus and will be no longer maintained. You may wish to install PMCMRplus instead.
library(vegan)
## Loading required package: permute
## Loading required package: lattice
## This is vegan 2.5-2
library(betapart) 
library(stringr)
library(permute) #Me pide que carge permute y lattice en el Rstudio que estoy usando
library(lattice)

# path to scripts Archnida and data
datafolder=setwd("~/Documents/Multihierarchical_NevadoToluca/bin/Arachnida")

#We get the diversity analysis at haplotypes, CL 3%, and CL 5% in Arachnida
source("3Com_matrixes_data_exploration_Arachnida_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.1640223 
## Run 1 stress 0.1679684 
## Run 2 stress 0.1739974 
## Run 3 stress 0.1683444 
## Run 4 stress 0.1645922 
## Run 5 stress 0.1742895 
## Run 6 stress 0.1663096 
## Run 7 stress 0.1691587 
## Run 8 stress 0.1765081 
## Run 9 stress 0.1703824 
## Run 10 stress 0.1667404 
## Run 11 stress 0.1766159 
## Run 12 stress 0.1881831 
## Run 13 stress 0.1664881 
## Run 14 stress 0.1651429 
## Run 15 stress 0.1778769 
## Run 16 stress 0.1651427 
## Run 17 stress 0.1668813 
## Run 18 stress 0.1795623 
## Run 19 stress 0.1701643 
## Run 20 stress 0.1649558 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("3Com_matrixes_data_exploration_Arachnida3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.1922801 
## Run 1 stress 0.1922832 
## ... Procrustes: rmse 0.0005256472  max resid 0.00241487 
## ... Similar to previous best
## Run 2 stress 0.1937837 
## Run 3 stress 0.1937837 
## Run 4 stress 0.192182 
## ... New best solution
## ... Procrustes: rmse 0.01610239  max resid 0.06966978 
## Run 5 stress 0.1922799 
## ... Procrustes: rmse 0.0160914  max resid 0.06970306 
## Run 6 stress 0.2090318 
## Run 7 stress 0.1921864 
## ... Procrustes: rmse 0.001686047  max resid 0.008211913 
## ... Similar to previous best
## Run 8 stress 0.2144559 
## Run 9 stress 0.2017443 
## Run 10 stress 0.1962925 
## Run 11 stress 0.204813 
## Run 12 stress 0.1937838 
## Run 13 stress 0.2113368 
## Run 14 stress 0.2017474 
## Run 15 stress 0.1937838 
## Run 16 stress 0.2117359 
## Run 17 stress 0.2051695 
## Run 18 stress 0.1922797 
## ... Procrustes: rmse 0.01610273  max resid 0.06963002 
## Run 19 stress 0.196664 
## Run 20 stress 0.2123748 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("3Com_matrixes_data_exploration_Arachnida5P_Site.R")
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.199876 
## Run 1 stress 0.2203456 
## Run 2 stress 0.1992482 
## ... New best solution
## ... Procrustes: rmse 0.02163884  max resid 0.08464907 
## Run 3 stress 0.223397 
## Run 4 stress 0.1992454 
## ... New best solution
## ... Procrustes: rmse 0.001427475  max resid 0.00815099 
## ... Similar to previous best
## Run 5 stress 0.1992468 
## ... Procrustes: rmse 0.0004223904  max resid 0.001952078 
## ... Similar to previous best
## Run 6 stress 0.2106065 
## Run 7 stress 0.2175375 
## Run 8 stress 0.2025484 
## Run 9 stress 0.2186123 
## Run 10 stress 0.2024495 
## Run 11 stress 0.2186139 
## Run 12 stress 0.2103359 
## Run 13 stress 0.2106104 
## Run 14 stress 0.2087461 
## Run 15 stress 0.1998754 
## Run 16 stress 0.1992457 
## ... Procrustes: rmse 0.0003666967  max resid 0.001487456 
## ... Similar to previous best
## Run 17 stress 0.2043646 
## Run 18 stress 0.2081462 
## Run 19 stress 0.2121891 
## Run 20 stress 0.2085521 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

# path to scripts Coleoptera and data
datafolder=setwd("~/Documents/Multihierarchical_NevadoToluca/bin/Coleoptera")

source("Com_matrixes_data_exploration_Coleoptera_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 9.552724e-05 
## Run 1 stress 9.787677e-05 
## ... Procrustes: rmse 0.0001970804  max resid 0.0006956024 
## ... Similar to previous best
## Run 2 stress 9.877437e-05 
## ... Procrustes: rmse 0.0001641056  max resid 0.0006501681 
## ... Similar to previous best
## Run 3 stress 9.869856e-05 
## ... Procrustes: rmse 0.0001318361  max resid 0.0003877093 
## ... Similar to previous best
## Run 4 stress 9.304418e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001609752  max resid 0.0006301323 
## ... Similar to previous best
## Run 5 stress 9.664324e-05 
## ... Procrustes: rmse 7.73205e-05  max resid 0.0001750782 
## ... Similar to previous best
## Run 6 stress 9.539234e-05 
## ... Procrustes: rmse 0.0001555808  max resid 0.0005018671 
## ... Similar to previous best
## Run 7 stress 9.726357e-05 
## ... Procrustes: rmse 0.0001978071  max resid 0.000497889 
## ... Similar to previous best
## Run 8 stress 7.737476e-05 
## ... New best solution
## ... Procrustes: rmse 0.0001766167  max resid 0.0005973825 
## ... Similar to previous best
## Run 9 stress 9.516042e-05 
## ... Procrustes: rmse 0.0001428192  max resid 0.0004594777 
## ... Similar to previous best
## Run 10 stress 9.761113e-05 
## ... Procrustes: rmse 0.0001312488  max resid 0.0004007721 
## ... Similar to previous best
## Run 11 stress 9.920261e-05 
## ... Procrustes: rmse 0.0001340527  max resid 0.0004238194 
## ... Similar to previous best
## Run 12 stress 9.560344e-05 
## ... Procrustes: rmse 0.0001915908  max resid 0.0005377258 
## ... Similar to previous best
## Run 13 stress 9.763345e-05 
## ... Procrustes: rmse 0.0001955837  max resid 0.0005730448 
## ... Similar to previous best
## Run 14 stress 9.708666e-05 
## ... Procrustes: rmse 0.0001991139  max resid 0.0006428978 
## ... Similar to previous best
## Run 15 stress 9.335531e-05 
## ... Procrustes: rmse 0.0001663727  max resid 0.0006094566 
## ... Similar to previous best
## Run 16 stress 9.487749e-05 
## ... Procrustes: rmse 0.0001035847  max resid 0.00023851 
## ... Similar to previous best
## Run 17 stress 9.863725e-05 
## ... Procrustes: rmse 0.0001062759  max resid 0.000485651 
## ... Similar to previous best
## Run 18 stress 9.133803e-05 
## ... Procrustes: rmse 0.0001779409  max resid 0.00062802 
## ... Similar to previous best
## Run 19 stress 9.497074e-05 
## ... Procrustes: rmse 8.768534e-05  max resid 0.0002337867 
## ... Similar to previous best
## Run 20 stress 9.461679e-05 
## ... Procrustes: rmse 0.0001404218  max resid 0.0004913111 
## ... Similar to previous best
## *** Solution reached
## Warning in metaMDS(beta.pair$beta.sim): stress is (nearly) zero: you may
## have insufficient data
## species scores not available

## Run 0 stress 0.1016899 
## Run 1 stress 0.1107812 
## Run 2 stress 0.1095616 
## Run 3 stress 0.1098187 
## Run 4 stress 0.1137073 
## Run 5 stress 0.1084474 
## Run 6 stress 0.1103595 
## Run 7 stress 0.1100515 
## Run 8 stress 0.1136891 
## Run 9 stress 0.1063241 
## Run 10 stress 0.1105762 
## Run 11 stress 0.1030998 
## Run 12 stress 0.1137284 
## Run 13 stress 0.1137937 
## Run 14 stress 0.1023525 
## Run 15 stress 0.1123426 
## Run 16 stress 0.1079861 
## Run 17 stress 0.1109042 
## Run 18 stress 0.1067707 
## Run 19 stress 0.1095911 
## Run 20 stress 0.1198716 
## *** No convergence -- monoMDS stopping criteria:
##      3: no. of iterations >= maxit
##     17: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Com_matrixes_data_exploration_Coleoptera_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.1296922 
## Run 1 stress 0.139895 
## Run 2 stress 0.1300206 
## ... Procrustes: rmse 0.05180756  max resid 0.2878262 
## Run 3 stress 0.1314035 
## Run 4 stress 0.1372969 
## Run 5 stress 0.1385894 
## Run 6 stress 0.1363449 
## Run 7 stress 0.1269966 
## ... New best solution
## ... Procrustes: rmse 0.08684451  max resid 0.2694403 
## Run 8 stress 0.134147 
## Run 9 stress 0.1235772 
## ... New best solution
## ... Procrustes: rmse 0.04965799  max resid 0.1573321 
## Run 10 stress 0.1317764 
## Run 11 stress 0.1254629 
## Run 12 stress 0.1344783 
## Run 13 stress 0.1389731 
## Run 14 stress 0.1415737 
## Run 15 stress 0.1324665 
## Run 16 stress 0.129953 
## Run 17 stress 0.1375635 
## Run 18 stress 0.1418608 
## Run 19 stress 0.1413945 
## Run 20 stress 0.1387772 
## *** No convergence -- monoMDS stopping criteria:
##      5: no. of iterations >= maxit
##     15: stress ratio > sratmax
## species scores not available

## species scores not available

## Run 0 stress 0.1398926 
## Run 1 stress 0.1384467 
## ... New best solution
## ... Procrustes: rmse 0.0386572  max resid 0.1214053 
## Run 2 stress 0.1330395 
## ... New best solution
## ... Procrustes: rmse 0.08190981  max resid 0.2827767 
## Run 3 stress 0.1409318 
## Run 4 stress 0.1496547 
## Run 5 stress 0.1352541 
## Run 6 stress 0.1434584 
## Run 7 stress 0.1420609 
## Run 8 stress 0.1455931 
## Run 9 stress 0.1334509 
## ... Procrustes: rmse 0.05960723  max resid 0.1805138 
## Run 10 stress 0.1451467 
## Run 11 stress 0.1485646 
## Run 12 stress 0.1412765 
## Run 13 stress 0.1461685 
## Run 14 stress 0.1334913 
## ... Procrustes: rmse 0.02238926  max resid 0.05375086 
## Run 15 stress 0.1461491 
## Run 16 stress 0.1449354 
## Run 17 stress 0.1352485 
## Run 18 stress 0.1370881 
## Run 19 stress 0.1354264 
## Run 20 stress 0.1547955 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Com_matrixes_data_exploration_Coleoptera_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site0.05$sample_richness_Site0.05, : Ties are present, p-values
## are not corrected.

## Run 0 stress 0.1400952 
## Run 1 stress 0.1413825 
## Run 2 stress 0.1435267 
## Run 3 stress 0.1436169 
## Run 4 stress 0.1379026 
## ... New best solution
## ... Procrustes: rmse 0.08712714  max resid 0.3348145 
## Run 5 stress 0.1388775 
## Run 6 stress 0.1397677 
## Run 7 stress 0.1458976 
## Run 8 stress 0.1408399 
## Run 9 stress 0.1415957 
## Run 10 stress 0.1442065 
## Run 11 stress 0.1443796 
## Run 12 stress 0.1409391 
## Run 13 stress 0.1392186 
## Run 14 stress 0.1400998 
## Run 15 stress 0.1410403 
## Run 16 stress 0.1461465 
## Run 17 stress 0.1437058 
## Run 18 stress 0.140968 
## Run 19 stress 0.142444 
## Run 20 stress 0.1420327 
## *** No convergence -- monoMDS stopping criteria:
##      7: no. of iterations >= maxit
##     13: stress ratio > sratmax
## species scores not available

## species scores not available

## Run 0 stress 0.1639448 
## Run 1 stress 0.1678622 
## Run 2 stress 0.1744525 
## Run 3 stress 0.1650347 
## Run 4 stress 0.1730234 
## Run 5 stress 0.1646985 
## Run 6 stress 0.170238 
## Run 7 stress 0.1739528 
## Run 8 stress 0.166885 
## Run 9 stress 0.1655843 
## Run 10 stress 0.1637101 
## ... New best solution
## ... Procrustes: rmse 0.01428983  max resid 0.05498424 
## Run 11 stress 0.1722356 
## Run 12 stress 0.1800045 
## Run 13 stress 0.1647536 
## Run 14 stress 0.1654806 
## Run 15 stress 0.1672895 
## Run 16 stress 0.1758105 
## Run 17 stress 0.171137 
## Run 18 stress 0.1835207 
## Run 19 stress 0.1693005 
## Run 20 stress 0.164257 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

# path to scripts Coleoptera and data
datafolder=setwd("~/Documents/Multihierarchical_NevadoToluca/bin/Collembola")

source("Com_matrixes_data_exploration_Collembola_h_Site.R") 
## Warning in Ops.factor(left, right): '>' not meaningful for factors
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site_h$sample_richness_Site_h, : Ties are present, p-values are
## not corrected.

## Run 0 stress 0.1042231 
## Run 1 stress 0.104223 
## ... New best solution
## ... Procrustes: rmse 0.0002040128  max resid 0.001180857 
## ... Similar to previous best
## Run 2 stress 0.1043388 
## ... Procrustes: rmse 0.08290892  max resid 0.1998987 
## Run 3 stress 0.1042235 
## ... Procrustes: rmse 0.0002939513  max resid 0.001700164 
## ... Similar to previous best
## Run 4 stress 0.1042229 
## ... New best solution
## ... Procrustes: rmse 4.525118e-05  max resid 0.000216953 
## ... Similar to previous best
## Run 5 stress 0.104338 
## ... Procrustes: rmse 0.009300536  max resid 0.05088375 
## Run 6 stress 0.1043394 
## ... Procrustes: rmse 0.009600235  max resid 0.05267211 
## Run 7 stress 0.1043085 
## ... Procrustes: rmse 0.08290456  max resid 0.2000942 
## Run 8 stress 0.1043086 
## ... Procrustes: rmse 0.08284508  max resid 0.2001466 
## Run 9 stress 0.1043388 
## ... Procrustes: rmse 0.0829341  max resid 0.1999117 
## Run 10 stress 0.1043362 
## ... Procrustes: rmse 0.08275477  max resid 0.2000689 
## Run 11 stress 0.1043131 
## ... Procrustes: rmse 0.004743172  max resid 0.02269677 
## Run 12 stress 0.1043103 
## ... Procrustes: rmse 0.08297293  max resid 0.2000156 
## Run 13 stress 0.1043091 
## ... Procrustes: rmse 0.08282211  max resid 0.2001727 
## Run 14 stress 0.1043085 
## ... Procrustes: rmse 0.08287234  max resid 0.2001345 
## Run 15 stress 0.1043087 
## ... Procrustes: rmse 0.08284307  max resid 0.2001469 
## Run 16 stress 0.1043085 
## ... Procrustes: rmse 0.08285937  max resid 0.2001342 
## Run 17 stress 0.1043087 
## ... Procrustes: rmse 0.08283982  max resid 0.2001509 
## Run 18 stress 0.1043084 
## ... Procrustes: rmse 0.08289331  max resid 0.2001032 
## Run 19 stress 0.1043087 
## ... Procrustes: rmse 0.08292533  max resid 0.2000699 
## Run 20 stress 0.1043389 
## ... Procrustes: rmse 0.08293913  max resid 0.1999162 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Com_matrixes_data_exploration_Collembola_3P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.1037297 
## Run 1 stress 0.1067374 
## Run 2 stress 0.1074049 
## Run 3 stress 0.1090234 
## Run 4 stress 0.1105674 
## Run 5 stress 0.1069449 
## Run 6 stress 0.1100534 
## Run 7 stress 0.1102973 
## Run 8 stress 0.1141589 
## Run 9 stress 0.1095515 
## Run 10 stress 0.1081166 
## Run 11 stress 0.1077708 
## Run 12 stress 0.1103508 
## Run 13 stress 0.1080835 
## Run 14 stress 0.1105674 
## Run 15 stress 0.1089478 
## Run 16 stress 0.1124763 
## Run 17 stress 0.1094777 
## Run 18 stress 0.110222 
## Run 19 stress 0.1149544 
## Run 20 stress 0.1102405 
## *** No convergence -- monoMDS stopping criteria:
##     20: stress ratio > sratmax
## species scores not available

## species scores not available

## species scores not available

## species scores not available

source("Com_matrixes_data_exploration_Collembola_5P_Site.R") 
## `summarise()` ungrouping output (override with `.groups` argument)

## Warning in posthoc.kruskal.nemenyi.test.default(x =
## richness_Site$sample_richness_Site, : Ties are present, p-values are not
## corrected.

## Run 0 stress 0.1206288 
## Run 1 stress 0.1207496 
## ... Procrustes: rmse 0.06438818  max resid 0.2126625 
## Run 2 stress 0.1289752 
## Run 3 stress 0.1263137 
## Run 4 stress 0.1262847 
## Run 5 stress 0.1209384 
## ... Procrustes: rmse 0.02715519  max resid 0.1660014 
## Run 6 stress 0.1345762 
## Run 7 stress 0.1215533 
## Run 8 stress 0.1273446 
## Run 9 stress 0.1213406 
## Run 10 stress 0.1247885 
## Run 11 stress 0.1239148 
## Run 12 stress 0.1268553 
## Run 13 stress 0.1217131 
## Run 14 stress 0.1209385 
## ... Procrustes: rmse 0.02716454  max resid 0.1659673 
## Run 15 stress 0.1206288 
## ... Procrustes: rmse 3.606555e-05  max resid 0.0001124391 
## ... Similar to previous best
## Run 16 stress 0.122796 
## Run 17 stress 0.1229115 
## Run 18 stress 0.1239098 
## Run 19 stress 0.1229116 
## Run 20 stress 0.1207594 
## ... Procrustes: rmse 0.06441344  max resid 0.212654 
## *** Solution reached
## species scores not available

## species scores not available

## species scores not available

## species scores not available

####################################END######################################################################